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- PDB-9f3k: Crystal structure of Kluyveromyces lactis glucokinase mutant H304... -

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Basic information

Entry
Database: PDB / ID: 9f3k
TitleCrystal structure of Kluyveromyces lactis glucokinase mutant H304Q in complex with glucose
ComponentsGlucokinase-1
KeywordsTRANSFERASE / sugar metabolism
Function / homology
Function and homology information


glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain
Similarity search - Domain/homology
beta-D-glucopyranose / MALONATE ION / Glucokinase-1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsWeisse, R.H. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1
Authors: Weisse, R.H. / Kettner, K. / Lilie, H. / Funk, L. / Roedel, G. / Tittmann, K. / Strater, N. / Kriegel, T.M.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase-1
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69911
Polymers107,6242
Non-polymers1,0759
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, equilibrium of monomer and homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint35 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.300, 205.300, 87.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 44 or resid 51 through 481 or resid 500 through 512))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA2 - 442 - 44
d_12GLYGLYTYRTYRAA51 - 48151 - 481
d_13BGCBGCBGCBGCAC501
d_14MLIMLIMLIMLIAD502
d_15MLIMLIMLIMLIAE503
d_16MLIMLIMLIMLIAF504
d_21SERSERTYRTYRBB2 - 4812 - 481
d_22BGCBGCBGCBGCBH501
d_23MLIMLIMLIMLIBI502
d_24MLIMLIMLIMLIBJ503
d_25MLIMLIMLIMLIBK504

NCS oper: (Code: givenMatrix: (-0.998524271458, 0.0289190009305, 0.0459670609644), (-0.0475421546307, -0.874601227375, -0.48250641095), (0.026249244591, -0.483979735588, 0.874685424995)Vector: 40. ...NCS oper: (Code: given
Matrix: (-0.998524271458, 0.0289190009305, 0.0459670609644), (-0.0475421546307, -0.874601227375, -0.48250641095), (0.026249244591, -0.483979735588, 0.874685424995)
Vector: 40.1463673622, 119.00638792, 29.3547772282)

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Components

#1: Protein Glucokinase-1 / Glucose kinase 1 / GLK-1 / Hexokinase GLK1


Mass: 53812.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: JA6 / Gene: GLK1, KLLA0C01155g / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6 / References: UniProt: Q6CUZ3, glucokinase, hexokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 9.8 mM glucose 9.8 mM DTT reservoir solution: 1.6 M sodium malonate pH 5.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→145.17 Å / Num. obs: 42518 / % possible obs: 99.3 % / Redundancy: 9 % / Biso Wilson estimate: 97.93 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.5
Reflection shellResolution: 2.85→2.96 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4410 / CC1/2: 0.282 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS1.dev.877-g8f078f0data reduction
Aimless0.5.31data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→64.92 Å / SU ML: 0.4565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 1087 2.56 %
Rwork0.2186 41357 -
obs0.219 42444 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.77 Å2
Refinement stepCycle: LAST / Resolution: 2.85→64.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 73 59 7620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027699
X-RAY DIFFRACTIONf_angle_d0.477810412
X-RAY DIFFRACTIONf_chiral_restr0.03761191
X-RAY DIFFRACTIONf_plane_restr0.00331352
X-RAY DIFFRACTIONf_dihedral_angle_d13.41172839
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.00340210181 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.980.39381360.42875086X-RAY DIFFRACTION98.29
2.98-3.140.33911340.31475150X-RAY DIFFRACTION99.87
3.14-3.330.25941280.27065197X-RAY DIFFRACTION99.74
3.33-3.590.29321240.27685098X-RAY DIFFRACTION98.03
3.59-3.950.22781220.21335206X-RAY DIFFRACTION99.83
3.95-4.520.20981490.19385171X-RAY DIFFRACTION99.48
4.52-5.70.19841300.19415203X-RAY DIFFRACTION99.03
5.7-64.920.22221640.19645246X-RAY DIFFRACTION98.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.12913531420.1894970941630.8206883222143.079860994980.6647615601412.290501035120.119758250969-0.454522799177-0.1027934628050.2166899600890.2060662767830.2856425360740.0386733142182-0.4653360932560.469165936060.662156144720.09386411066170.04777264800841.03514123580.05221547003340.9917247127694.0507567823769.5028561388.780178082
20.504281844282-0.8959994247820.4760600641942.287813396210.08362444549541.98043687020.0839741716785-0.0358987300176-0.23585778866-0.624725131923-0.003047549374160.459843707495-0.00582807963152-0.3184468106030.000107222736860.804322311531-0.0676925554286-0.2817941313261.088447283690.00659277980951.16871211398-5.6382565345370.2316056935-14.8229758771
31.58672730105-0.459304911151-0.160480976332.742425614070.1667551896591.687615389290.238025913894-0.10214476503-0.0621355613695-0.0890669304095-0.06959409589220.2368011774160.2229438652590.02278218809461.56590416062E-50.775212090740.251067967407-0.1348211367010.738557305169-0.1132823867910.58371629115937.996019900553.49525351893.33138758461
41.805506010490.378998551864-0.4710464947391.278318612540.3168864684693.955106736230.1282778170810.2429954382720.0773254980628-0.625969265401-0.0892155012222-0.0884506093118-0.358473082787-0.148344741846-3.02997337985E-50.9663483744830.3230267682860.06931149120870.923627268992-0.05446826582280.72844533494447.230233615865.0714428753-17.8325498096
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resi 2:63 or resi 205:463)AA2 - 4632 - 462
22chain A and (resi 64:204 or resi 464:481)AA64 - 48163 - 480
33chain B and (resi 2:63 or resi 205:463)BH2 - 4632 - 456
44chain B and (resi 64:204 or resi 464:481)BH64 - 48157 - 474

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